Atomistry » Rhodium » PDB 165d-8oqd » 7qpz
Atomistry »
  Rhodium »
    PDB 165d-8oqd »
      7qpz »

Rhodium in PDB 7qpz: X-Ray Structure of the Adduct Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Rnase A (4)

Enzymatic activity of X-Ray Structure of the Adduct Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Rnase A (4)

All present enzymatic activity of X-Ray Structure of the Adduct Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Rnase A (4):
4.6.1.18;

Protein crystallography data

The structure of X-Ray Structure of the Adduct Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Rnase A (4), PDB code: 7qpz was solved by D.Loreto, A.Merlino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.86 / 1.45
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 100.73, 32.87, 72.89, 90, 90.15, 90
R / Rfree (%) 16.2 / 20.2

Other elements in 7qpz:

The structure of X-Ray Structure of the Adduct Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Rnase A (4) also contains other interesting chemical elements:

Fluorine (F) 3 atoms

Rhodium Binding Sites:

The binding sites of Rhodium atom in the X-Ray Structure of the Adduct Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Rnase A (4) (pdb code 7qpz). This binding sites where shown within 5.0 Angstroms radius around Rhodium atom.
In total 8 binding sites of Rhodium where determined in the X-Ray Structure of the Adduct Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Rnase A (4), PDB code: 7qpz:
Jump to Rhodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Rhodium binding site 1 out of 8 in 7qpz

Go back to Rhodium Binding Sites List in 7qpz
Rhodium binding site 1 out of 8 in the X-Ray Structure of the Adduct Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Rnase A (4)


Mono view


Stereo pair view

A full contact list of Rhodium with other atoms in the Rh binding site number 1 of X-Ray Structure of the Adduct Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Rnase A (4) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rh201

b:16.8
occ:0.75
 RH1 A:F5T201 0.0 16.8 0.8
O1 A:F5T201 2.1 16.6 0.8
O7 A:F5T201 2.1 17.0 0.8
O3 A:F5T201 2.1 19.6 0.8
O A:HOH356 2.1 18.7 0.8
O0 A:F5T201 2.1 18.9 0.8
RH2 A:F5T201 2.4 11.8 0.8
C5 A:F5T201 2.9 24.6 0.8
C3 A:F5T201 2.9 15.9 0.8
C1 A:F5T201 3.0 14.0 0.8
O2 A:F5T201 3.1 14.0 0.8
O8 A:F5T201 3.1 14.8 0.8
O4 A:F5T201 3.2 16.2 0.8
O9 A:F5T201 3.2 15.6 0.8
HZ3 A:LYS7 3.7 27.9 1.0
HD1 A:HIS119 3.8 10.5 0.0
O A:HOH418 4.1 24.9 1.0
HE2 A:LYS7 4.2 24.5 1.0
HZ2 A:LYS7 4.3 27.9 1.0
C6 A:F5T201 4.3 33.2 0.8
NZ A:LYS7 4.4 29.5 1.0
C4 A:F5T201 4.4 16.5 0.8
C2 A:F5T201 4.4 13.9 0.8
O A:HOH367 4.5 13.8 0.3
ND1 A:HIS119 4.6 10.5 1.0
O A:HOH310 4.7 30.8 1.0
O A:HOH465 4.7 29.8 1.0
CE A:LYS7 4.8 24.7 1.0
HD3 A:LYS7 4.8 20.0 1.0
HB2 A:HIS119 4.8 9.5 1.0
F1 A:F5T201 4.8 33.5 0.8
F3 A:F5T201 4.8 41.5 0.8

Rhodium binding site 2 out of 8 in 7qpz

Go back to Rhodium Binding Sites List in 7qpz
Rhodium binding site 2 out of 8 in the X-Ray Structure of the Adduct Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Rnase A (4)


Mono view


Stereo pair view

A full contact list of Rhodium with other atoms in the Rh binding site number 2 of X-Ray Structure of the Adduct Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Rnase A (4) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rh201

b:11.8
occ:0.75
 RH2 A:F5T201 0.0 11.8 0.8
HD1 A:HIS119 1.4 10.5 0.0
O2 A:F5T201 2.1 14.0 0.8
O4 A:F5T201 2.1 16.2 0.8
O8 A:F5T201 2.1 14.8 0.8
O9 A:F5T201 2.1 15.6 0.8
ND1 A:HIS119 2.3 10.5 1.0
RH1 A:F5T201 2.4 16.8 0.8
C5 A:F5T201 2.9 24.6 0.8
C3 A:F5T201 2.9 15.9 0.8
C1 A:F5T201 3.0 14.0 0.8
HB2 A:HIS119 3.0 9.5 1.0
O0 A:F5T201 3.1 18.9 0.8
O1 A:F5T201 3.1 16.6 0.8
O7 A:F5T201 3.1 17.0 0.8
O3 A:F5T201 3.2 19.6 0.8
CE1 A:HIS119 3.2 12.9 1.0
HE1 A:HIS119 3.3 11.9 1.0
CG A:HIS119 3.3 10.1 1.0
CB A:HIS119 3.6 9.5 1.0
O A:HOH329 3.9 12.2 1.0
HA A:HIS119 3.9 8.7 1.0
O A:HOH395 4.1 20.4 1.0
NE2 A:HIS119 4.3 11.5 1.0
C6 A:F5T201 4.3 33.2 0.8
C4 A:F5T201 4.4 16.5 0.8
CA A:HIS119 4.4 8.8 1.0
C2 A:F5T201 4.4 13.9 0.8
CD2 A:HIS119 4.4 11.6 1.0
HB3 A:HIS119 4.4 9.4 1.0
O A:HOH356 4.4 18.7 0.8
O A:HOH310 4.5 30.8 1.0
O A:VAL118 4.6 10.2 1.0
O A:HOH389 4.7 23.0 1.0
F2 A:F5T201 4.7 43.6 0.8
O A:HOH472 4.8 37.7 1.0
O A:HOH402 4.8 36.4 1.0
O A:HOH303 4.8 38.7 1.0
F3 A:F5T201 4.9 41.5 0.8
H A:PHE120 4.9 7.9 1.0

Rhodium binding site 3 out of 8 in 7qpz

Go back to Rhodium Binding Sites List in 7qpz
Rhodium binding site 3 out of 8 in the X-Ray Structure of the Adduct Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Rnase A (4)


Mono view


Stereo pair view

A full contact list of Rhodium with other atoms in the Rh binding site number 3 of X-Ray Structure of the Adduct Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Rnase A (4) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rh202

b:21.3
occ:0.55
 RH1 A:F5I202 0.0 21.3 0.6
O6 A:F5I202 2.1 22.6 0.6
O7 A:F5I202 2.1 19.8 0.6
O1 A:F5I202 2.1 18.9 0.6
O3 A:F5I202 2.1 20.1 0.6
O A:HOH449 2.3 22.4 0.6
RH2 A:F5I202 2.4 13.5 0.6
C1 A:F5I202 2.9 20.1 0.6
C3 A:F5I202 2.9 19.9 0.6
O8 A:F5I202 3.0 16.9 0.6
O2 A:F5I202 3.1 15.1 0.6
O5 A:F5I202 3.1 18.2 0.6
O4 A:F5I202 3.2 19.1 0.6
HE2 A:HIS105 3.7 12.5 0.0
C4 A:F5I202 4.4 19.3 0.6
C2 A:F5I202 4.4 17.7 0.6
O A:HOH314 4.6 43.1 1.0
NE2 A:HIS105 4.6 12.5 1.0
O A:HOH451 4.6 43.2 1.0
O A:HOH505 4.9 28.4 1.0

Rhodium binding site 4 out of 8 in 7qpz

Go back to Rhodium Binding Sites List in 7qpz
Rhodium binding site 4 out of 8 in the X-Ray Structure of the Adduct Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Rnase A (4)


Mono view


Stereo pair view

A full contact list of Rhodium with other atoms in the Rh binding site number 4 of X-Ray Structure of the Adduct Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Rnase A (4) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rh202

b:13.5
occ:0.55
 RH2 A:F5I202 0.0 13.5 0.6
HE2 A:HIS105 1.3 12.5 0.0
O5 A:F5I202 2.1 18.2 0.6
O2 A:F5I202 2.1 15.1 0.6
O4 A:F5I202 2.1 19.1 0.6
O8 A:F5I202 2.1 16.9 0.6
NE2 A:HIS105 2.2 12.5 1.0
RH1 A:F5I202 2.4 21.3 0.6
C1 A:F5I202 2.9 20.1 0.6
C3 A:F5I202 3.0 19.9 0.6
O3 A:F5I202 3.1 20.1 0.6
O1 A:F5I202 3.1 18.9 0.6
CE1 A:HIS105 3.1 12.9 1.0
O7 A:F5I202 3.2 19.8 0.6
O6 A:F5I202 3.2 22.6 0.6
CD2 A:HIS105 3.2 12.6 1.0
HE1 A:HIS105 3.3 12.7 1.0
HD2 A:HIS105 3.4 12.1 1.0
O A:HOH316 4.0 33.0 1.0
O A:HOH434 4.2 43.5 1.0
HG21 A:THR78 4.3 14.0 1.0
ND1 A:HIS105 4.3 12.3 1.0
O A:HOH360 4.3 22.6 1.0
CG A:HIS105 4.3 10.6 1.0
HG23 A:THR78 4.3 14.0 1.0
C2 A:F5I202 4.4 17.7 0.6
C4 A:F5I202 4.5 19.3 0.6
O A:HOH314 4.5 43.1 1.0
CG2 A:THR78 4.7 14.3 1.0
HG22 A:THR78 4.7 14.0 1.0
O A:HOH449 4.8 22.4 0.6

Rhodium binding site 5 out of 8 in 7qpz

Go back to Rhodium Binding Sites List in 7qpz
Rhodium binding site 5 out of 8 in the X-Ray Structure of the Adduct Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Rnase A (4)


Mono view


Stereo pair view

A full contact list of Rhodium with other atoms in the Rh binding site number 5 of X-Ray Structure of the Adduct Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Rnase A (4) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Rh201

b:13.0
occ:0.30
 RH1 B:F5I201 0.0 13.0 0.3
RH1 B:F5I201 0.6 13.7 0.3
HD1 B:HIS119 1.5 15.9 0.0
O3 B:F5I201 1.6 18.8 0.3
O6 B:F5I201 1.9 14.5 0.3
O1 B:F5I201 2.1 13.9 0.3
O3 B:F5I201 2.1 14.4 0.3
O7 B:F5I201 2.1 14.3 0.3
O6 B:F5I201 2.1 15.5 0.3
ND1 B:HIS119 2.3 15.9 1.0
RH2 B:F5I201 2.4 18.5 0.3
RH2 B:F5I201 2.4 16.7 0.3
O7 B:F5I201 2.4 15.9 0.3
O1 B:F5I201 2.6 16.1 0.3
O4 B:F5I201 2.8 19.4 0.3
C1 B:F5I201 2.9 13.3 0.3
O2 B:F5I201 2.9 14.2 0.3
O5 B:F5I201 3.0 18.5 0.3
CE1 B:HIS119 3.1 18.6 1.0
O5 B:F5I201 3.1 17.8 0.3
HE1 B:HIS119 3.1 17.8 1.0
O2 B:F5I201 3.1 17.1 0.3
C3 B:F5I201 3.1 14.8 0.3
O8 B:F5I201 3.1 16.8 0.3
C3 B:F5I201 3.2 16.2 0.3
C1 B:F5I201 3.2 15.9 0.3
O4 B:F5I201 3.3 16.0 0.3
HB2 B:HIS119 3.3 11.6 1.0
CG B:HIS119 3.4 15.2 1.0
O8 B:F5I201 3.4 15.1 0.3
O B:HOH306 3.7 15.7 1.0
HA B:HIS119 3.7 9.5 1.0
CB B:HIS119 3.8 11.2 1.0
O B:HOH441 4.2 28.6 1.0
NE2 B:HIS119 4.3 18.5 1.0
CA B:HIS119 4.3 9.6 1.0
C2 B:F5I201 4.3 12.6 0.3
CD2 B:HIS119 4.4 16.0 1.0
C4 B:F5I201 4.5 14.0 0.3
O B:VAL118 4.6 11.1 1.0
O B:HOH402 4.6 34.0 1.0
H B:PHE120 4.6 9.1 1.0
C4 B:F5I201 4.6 17.0 0.3
HB3 B:HIS119 4.7 11.6 1.0
C2 B:F5I201 4.7 15.3 0.3
O B:HOH386 4.7 21.5 0.6
O B:HOH334 4.7 10.9 0.4
O B:HOH409 4.8 34.7 1.0
O B:HOH371 4.8 19.3 1.0
O B:HOH304 4.9 37.3 1.0

Rhodium binding site 6 out of 8 in 7qpz

Go back to Rhodium Binding Sites List in 7qpz
Rhodium binding site 6 out of 8 in the X-Ray Structure of the Adduct Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Rnase A (4)


Mono view


Stereo pair view

A full contact list of Rhodium with other atoms in the Rh binding site number 6 of X-Ray Structure of the Adduct Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Rnase A (4) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Rh201

b:13.7
occ:0.30
 RH1 B:F5I201 0.0 13.7 0.3
RH1 B:F5I201 0.6 13.0 0.3
HD1 B:HIS119 1.4 15.9 0.0
O7 B:F5I201 1.7 14.3 0.3
O3 B:F5I201 1.8 14.4 0.3
O1 B:F5I201 2.1 16.1 0.3
O6 B:F5I201 2.1 14.5 0.3
O7 B:F5I201 2.1 15.9 0.3
O3 B:F5I201 2.1 18.8 0.3
ND1 B:HIS119 2.3 15.9 1.0
RH2 B:F5I201 2.4 16.7 0.3
O1 B:F5I201 2.4 13.9 0.3
RH2 B:F5I201 2.5 18.5 0.3
O6 B:F5I201 2.6 15.5 0.3
C3 B:F5I201 2.7 14.8 0.3
C1 B:F5I201 2.8 15.9 0.3
O2 B:F5I201 2.8 17.1 0.3
C3 B:F5I201 2.9 16.2 0.3
O8 B:F5I201 3.0 16.8 0.3
HB2 B:HIS119 3.0 11.6 1.0
O4 B:F5I201 3.0 16.0 0.3
CE1 B:HIS119 3.1 18.6 1.0
O2 B:F5I201 3.1 14.2 0.3
O8 B:F5I201 3.1 15.1 0.3
C1 B:F5I201 3.2 13.3 0.3
HE1 B:HIS119 3.2 17.8 1.0
CG B:HIS119 3.3 15.2 1.0
O4 B:F5I201 3.3 19.4 0.3
O5 B:F5I201 3.3 18.5 0.3
O5 B:F5I201 3.4 17.8 0.3
CB B:HIS119 3.6 11.2 1.0
O B:HOH441 3.7 28.6 1.0
HA B:HIS119 3.8 9.5 1.0
C4 B:F5I201 4.1 14.0 0.3
O B:HOH306 4.1 15.7 1.0
CA B:HIS119 4.2 9.6 1.0
NE2 B:HIS119 4.2 18.5 1.0
C2 B:F5I201 4.3 15.3 0.3
CD2 B:HIS119 4.3 16.0 1.0
C4 B:F5I201 4.4 17.0 0.3
HB3 B:HIS119 4.4 11.6 1.0
O B:VAL118 4.4 11.1 1.0
O B:HOH409 4.5 34.7 1.0
C2 B:F5I201 4.6 12.6 0.3
O B:HOH386 4.7 21.5 0.6
H B:PHE120 4.9 9.1 1.0

Rhodium binding site 7 out of 8 in 7qpz

Go back to Rhodium Binding Sites List in 7qpz
Rhodium binding site 7 out of 8 in the X-Ray Structure of the Adduct Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Rnase A (4)


Mono view


Stereo pair view

A full contact list of Rhodium with other atoms in the Rh binding site number 7 of X-Ray Structure of the Adduct Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Rnase A (4) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Rh201

b:16.7
occ:0.30
 RH2 B:F5I201 0.0 16.7 0.3
RH2 B:F5I201 0.6 18.5 0.3
O2 B:F5I201 1.7 17.1 0.3
O8 B:F5I201 1.8 16.8 0.3
O8 B:F5I201 2.1 15.1 0.3
O5 B:F5I201 2.1 18.5 0.3
O4 B:F5I201 2.1 16.0 0.3
O2 B:F5I201 2.1 14.2 0.3
RH1 B:F5I201 2.4 13.7 0.3
RH1 B:F5I201 2.4 13.0 0.3
O B:HOH386 2.4 21.5 0.6
O5 B:F5I201 2.5 17.8 0.3
O4 B:F5I201 2.6 19.4 0.3
C1 B:F5I201 2.6 15.9 0.3
C3 B:F5I201 2.6 16.2 0.3
O7 B:F5I201 2.7 14.3 0.3
C3 B:F5I201 2.7 14.8 0.3
O7 B:F5I201 2.9 15.9 0.3
O3 B:F5I201 3.0 14.4 0.3
O1 B:F5I201 3.0 16.1 0.3
O3 B:F5I201 3.0 18.8 0.3
C1 B:F5I201 3.0 13.3 0.3
O1 B:F5I201 3.3 13.9 0.3
O6 B:F5I201 3.3 14.5 0.3
O6 B:F5I201 3.4 15.5 0.3
O B:HOH400 3.7 44.0 1.0
HZ3 B:LYS7 3.8 23.6 1.0
HD1 B:HIS119 3.8 15.9 0.0
O B:HOH448 4.0 36.9 1.0
C2 B:F5I201 4.0 15.3 0.3
C4 B:F5I201 4.1 17.0 0.3
HZ2 B:LYS7 4.2 23.6 1.0
C4 B:F5I201 4.2 14.0 0.3
HE2 B:LYS7 4.2 20.3 1.0
O B:HOH481 4.3 40.6 1.0
HD3 B:LYS7 4.3 16.4 1.0
NZ B:LYS7 4.3 25.5 1.0
C2 B:F5I201 4.5 12.6 0.3
ND1 B:HIS119 4.6 15.9 1.0
O B:HOH321 4.6 21.4 1.0
CE B:LYS7 4.7 19.9 1.0
HB2 B:HIS119 4.8 11.6 1.0

Rhodium binding site 8 out of 8 in 7qpz

Go back to Rhodium Binding Sites List in 7qpz
Rhodium binding site 8 out of 8 in the X-Ray Structure of the Adduct Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Rnase A (4)


Mono view


Stereo pair view

A full contact list of Rhodium with other atoms in the Rh binding site number 8 of X-Ray Structure of the Adduct Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Rnase A (4) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Rh201

b:18.5
occ:0.30
 RH2 B:F5I201 0.0 18.5 0.3
RH2 B:F5I201 0.6 16.7 0.3
O5 B:F5I201 1.7 18.5 0.3
O2 B:F5I201 1.8 14.2 0.3
O5 B:F5I201 2.1 17.8 0.3
O2 B:F5I201 2.1 17.1 0.3
O8 B:F5I201 2.1 16.8 0.3
O4 B:F5I201 2.1 19.4 0.3
RH1 B:F5I201 2.4 13.0 0.3
O B:HOH386 2.4 21.5 0.6
RH1 B:F5I201 2.5 13.7 0.3
O4 B:F5I201 2.6 16.0 0.3
O8 B:F5I201 2.6 15.1 0.3
C1 B:F5I201 2.7 13.3 0.3
O3 B:F5I201 2.8 18.8 0.3
O1 B:F5I201 3.0 13.9 0.3
O7 B:F5I201 3.0 14.3 0.3
C3 B:F5I201 3.0 16.2 0.3
O6 B:F5I201 3.1 15.5 0.3
C1 B:F5I201 3.1 15.9 0.3
O6 B:F5I201 3.2 14.5 0.3
C3 B:F5I201 3.2 14.8 0.3
O7 B:F5I201 3.2 15.9 0.3
O3 B:F5I201 3.2 14.4 0.3
O1 B:F5I201 3.4 16.1 0.3
HZ3 B:LYS7 3.4 23.6 1.0
HE2 B:LYS7 3.7 20.3 1.0
HZ2 B:LYS7 3.7 23.6 1.0
HD1 B:HIS119 3.8 15.9 0.0
NZ B:LYS7 3.9 25.5 1.0
HD3 B:LYS7 4.0 16.4 1.0
O B:HOH448 4.1 36.9 1.0
C2 B:F5I201 4.1 12.6 0.3
CE B:LYS7 4.2 19.9 1.0
O B:HOH400 4.2 44.0 1.0
C4 B:F5I201 4.5 17.0 0.3
C2 B:F5I201 4.5 15.3 0.3
O B:HOH481 4.5 40.6 1.0
O B:HOH321 4.6 21.4 1.0
ND1 B:HIS119 4.6 15.9 1.0
CD B:LYS7 4.7 16.8 1.0
C4 B:F5I201 4.7 14.0 0.3
HE21 B:GLN11 4.7 19.7 1.0
HZ1 B:LYS7 4.8 23.6 1.0
O B:HOH371 4.8 19.3 1.0
O B:HOH334 4.9 10.9 0.4

Reference:

D.Loreto, A.Esposito, N.Demitri, A.Guaragna, A.Merlino. Reactivity of A Fluorine-Containing Dirhodium Tetracarboxylate Compound with Proteins. Dalton Trans V. 51 3695 2022.
ISSN: ESSN 1477-9234
PubMed: 35166290
DOI: 10.1039/D2DT00082B
Page generated: Thu Oct 10 12:37:37 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy